Bio-Nano-Machines for Space Applications

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Bio-Nano-Machines for Space Applications

• Presented by Ajay Ummat (Graduate Student,
  Northeastern University, Boston)
• PI Constantinos Mavroidis, Ph.D., Associate
  Professor
• Computational Bio Nanorobotics Laboratory (CBNL)
• Dept. of Mechanical Industrial Engineering,
  Northeastern University, Boston, Massachusetts

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Researchers

Computational
Experimental
Dr. M. Yarmush Professor, Biomedical Engineering,
Rutgers University and MGH
Dr. C. Mavroidis Associate Professor Mechanical
Engineering, Northeastern University
Ajay Ummat PhD StudentNortheastern University
Kaushal Rege Research Fellow MGH / Shriners
Monica Casali Research Fellow MGH / Shriners
Zak Megeed Research AssociateMGH / Shriners
Atul Dubey PhD Student Rutgers University
Gaurav Sharma PhD Student Northeastern
University
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Consultants
Computational
Biology and Biomedical Engineering
Dr. Marianna Bei, MGH
Dr. Elias Gyftopoulos, MIT
Dr. John Kundert-Gibbs, Clemson University
Dr. Jeff Ruberti, NU
Dr. David Budil, NU
Dr. Silvina Tomassone, Rutgers
Chemistry and Chemical Engineering
Micro / Nano Manufacturing
Dr. Ahmed Busnaina, NU
Dr. Albert Sacco, NU
Dr. Demetri Papageorgiou, NU
Dr. Fotis Papadimitrakopoulos, UCONN
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Introduction and Objectives

• Identify and study computationally and
  experimentally protein and DNA configurations
  that can be used as bio-nano-machine components
• Design two macro-scale devices with important
  space application that will be using
  bio-nano-component assemblies
• The Networked TerraXplorer (NTXp)
• All Terrain Astronaut Bio-Nano Gears (ATB)

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The Roadmap
Automatic fabrication and information processing
Bio Sensors
A bio nano computational cell
Distributive intelligence programming control
A bio nano robot Representative Assembly of bio
components
DNA Joints
A Bio nano information processing component
Assembled bio nanorobots
HA a-helix
Bio nano components
Conceptual automatic information floor
Bio nano swarms
STEP 1
STEP 2
STEP 3
STEP 4
Research Progression
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Space Applications

• Our current research is focused on two main space
  based applications
• Networked TerraXplorers (NTXp)
• Mapping and sensing of vast planetary terrains
• All Terrain Astronaut Bionano Gears (ATB)
• Space radiation detection protection system

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Space Conditions / Design Requirements
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Space Atmospheric Environment

• Targeting Martian environment
• Atmosphere ? Carbon-di-oxide for energy
  production for bionano robots.
• Certain micro organisms Methanogens (H
  CO2)
• Temperature ? -140 to 20 degree C (require
  thermal insulation and thermally stable
  bio-components)
• Pressure ? 6.8 millibars as high as 9.0 millibars
  (1000 millibars on earth)
• Materials of sustaining internal pressures
• Bio-components which can sustain in lower
  pressures
• Transport mechanism through skin layer (NTXp)

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Space Conditions

• Topography ? Scale of the bio nano machines
  (within meters or miles) and the area of landing
  and deployment
• Local dust storms ? The design for NTXp capable
  of flowing through the local storms or resist it
  or both
• Radiation ? UV radiations between the wavelengths
  of 190 and 300 nm.
• Strong oxidants on the upper surface of Mars
  (radiation resistant and oxidant resistant
  skins!)

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Identification of Bionano Components

• Focusing on components from micro-organisms
• A positive correlation -
• The degree of stability of the organism ? The
  degree of stability of their proteins
• Studying enzymes (for their dynamics and model
  and ease of accessibility)
• - One key component is - RNA Polymerase
• - Found in many micro organisms - Thermoplasma
  acidophilum, Sulfolobus acidocaldarius,
  Thermoproteus tenax, Desulfurococcus mucosus

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Extreme Micro - Organisms
D. radiodurans

• Deinococcus radiodurans
• Cold-acclimation protein a protein from
• Pseudomonas
• Some key attributes required for the
• bio nano machines and components
• Radiation resistant
• Thermal resistance (high / low)
• Acidic environment resistant
• Dry condition resistant

Halobacterium
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Computational Framework
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Characterization of Bionano Components

• A control mechanism (chemical pathway) and its
  dependency on external parameters (such as, pH,
  temperature, chemical signals, enzymes)
• The change in the external environment triggers
  changes in the bionano component
• - conformation changes
• - variations in the pattern of their
  self-assembly
• These changes (for instance) demonstrate motion
  and a desired trajectory
• Reversibility
• Synchronization of individual bio-components
• Stochastic, less understood dynamics, complex
  chemical pathways

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Computational Framework

• Identification of the protein from the mentioned
  organisms ? characterization with respect to the
  following three main parameters
• - high temperature variations
• - dry conditions
• - space radiations
• Stability analysis ? Stability in various
  conditions is desired, such as, dry conditions,
  high temperature variations and radiations.
• The overall stability is a complex variable of
  all the individual stabilities

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Framework for bio molecular dynamics
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Reversibility Dynamics

• Reversibility dynamics in context of Variational
  dynamics

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Space Radiations on Bionano System

• Radiations can produce many effects
• break bonds, change the structure, destroy the
  amino acid residues, form other bonds
• Coupling of radiation at atomic level
• Hamiltonian for Radiation is coupled to the
  atomic system
• the term coupling the electrons of the atom
  with the radiation. Radiations can produce many
  effects
• break bonds, change the structure, destroy the
  amino acid residues, form other bonds
• is the sum of A coupling terms Hn ?

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Space Applications Networked TerraXplorers
(NTXp)
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Networked TerraXplorers (NTXp)Mapping of vast
planetary terrains
A realistic scenario where the Networked
TerraXplorers (NTXp) are employed. These meshes
would be launched through the parachute and these
would be spread open on the target surface. These
NTXps could be launched in large quantities
(hundreds) and hence the target terrain could be
thoroughly mapped and sensed. A single NTXp could
run into miles and when integrated with other
NTXPs could cover a vast terrain.
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Detailed Mechanism of NTXp
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System Level Design of NTXp
A
C
B
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Design Parameters Constraints

• External sensing ? Creation of tough external
  micro channels
• Reaction initiation ? Presence of charges (/-)
  on the NTXp surface
• Skin ? Existence of an external insulating and
  radiation resistive layers
• Intermediary exchange layer ? Small tubular
  structure for enabling active transport of ions
  or charges across
• - Connecting the micro channels and the bio-nano
  sensory module.
• Inner sensing layer ? Sensing the absorbed
  constituents and transferring the information of
  the measured parameters to the signaling module.

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Sensor Signal Dynamics

• Capable of converting the sensed parameter to a
  parameter which could be used for signaling
• Form ? flow of electrons, or variations in the
  concentration of ions and their gradients

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Flow of Signaling Parameters

• This correspondence table decodes the input
  variables, f and g (or more) into pure signaling
  variables, say, (x, y, z).
• Decoding ? reaction between the sensory input
  and the signaling module

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Nanofluidic Transport Mechanisms

• Nanofluidics actuator / pump for NTXp transport
  mechanism

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Space Applications All Terrain Bionano (ATB)
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The All Terrain Bionano (ATB) Gears for Astronauts
Outer Layer Interacting with the Space Suit
Middle Layer Signaling Information Storage
Inner Layer Interacting with the Astronaut
The layered concept of the ATB gears. Shown are
three layers for the ATB gears. The inner layer
would be in contact with the human body and the
outer layer would be responsible of sensing the
outer environment. The middle layer would be
responsible for communicating, signaling and drug
delivery.
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Space Radiation Molecular Damage

• Space radiation damage to DNA, breaking of
  bonds, mutations leading to cancerous conditions
• Monitoring of the space radiations for the
  astronauts is the key requirements. Our existing
  design deals with radiation detection

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Equivalence of Damage Effects

• Health hazards from the space radiations -
  creating equivalence energetically

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System Level Design of ATB
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Overall Structure of Layer A on the ATB

• Structure of the Layer A vertical as well as
  horizontal directions
• Non continuum design (in patches)
• Complimentary acceptor layer for electronic
  connections

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Design of Layer - A

• A surface view of the radiation detection layer
  the probabilistic reaction layer is represented
  by spheres.

• The molecular components utilized to make these
  reaction pathways
• Survival of the molecular component

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The Number Game Homological Settings

• Represents maximum probability regime for the
  reaction.
• Contains all the machinery (bionano robots)
  which will react with the radiation

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Probabilistic Reaction Centers

• Sphere ? modular design strategy
• Probabilistic arrangement of radiation reactants
  and their signaling pathways
• Electron / ionic transport reactions

Fe e- Fe
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Electron Transfer Reactions

• Electron transfer reactions plays a key role in
  bioenergetics
• Fermis Golden Rule describes the rates of the
  reactions
• Light (radiation?) triggered electron transfer
  initiation ? takes place in the reaction centers
  of the Layer A

Structure Of The Photosynthetic Reaction Centre
From Rhodobacter Sphaeroides Carotenoidless
Strain R-26.1
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Radiation Resistant Bacteria

• The many characteristics of D. radiodurans
• An extreme resistance to genotoxic chemicals
• Resistance to oxidative damage
• Resistance to high levels of ionizing and
  ultraviolet radiation
• Resistance to dehydration
• A cell wall forming three or more layers
• Repairs chromosome fragments, within 12-24
  hours
• Uses a two-system process
• i. Single-strand annealing ? single strand
  re-connections
• ii. Homologous recombination ?
  double-strand patch up
• RecA protein ? responsible for patch up and
  associated reactions for DNA repair
• This bacterium might contain space resistant
  proteins and other mechanisms

Deinococcus radiodurans
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Experimental Work

• Peptide Selection Loop 36 (chain of 36 amino
  acids)
• Protein Expression
• Protein Purification
• Site-Directed Mutagenesis
• Characterization of Protein Conformation as a
  Function of pH - Circular
  Dichroism Spectroscopy -
  Nuclear Magnetic Resonance (still to perform)

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Future Activities

• ATB gears for astronauts
  a) Design the reaction mechanism for radiation
  detection for ATB b)
  Design a detector layer complimentary to the
  Layer A c) Integration
  with the electronic systems
• NTXp a) Surface
  chemistry (water / mineral) detection network
  b)
  Multi channel pumping / actuating mechanism for
  transport c) Space
  condition tolerant outer skin for NTXp

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Future Activities

• Computational framework a) Integrate homology
  modeling of protein to expedite the design
  process b)
  Computationally analyze the effect of radiation
  c) Analyzing the
  radiation effects in ATB and how the ion /
  electron transfer effects could be related to
  intensity of radiation damage.
• Experimental a)
  Characterization of various bio-nano components
  b) Techniques
  from NMR would be used to exactly characterize
  the peptide structure when it changes its
  conformation c)
  Explore the radiation resistant bacterium
  Deinococcus radiodurans for possible radiation
  resistant bio-mechanisms and proteins d)
  Experiments with carbon nano tube structures and
  bio-nano components

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Publications / Presentations

• Chapter in CRC Handbook on Biomimetics -
  Biologically Inspired Technologies,
  Editor Yoseph Bar-Cohen, JPL
• Chapter in The Biomedical Engineering
  Handbook, 3rd Edition, Editor M. L.
  Yarmush,
• Paper Presented at the 7th NASA/DoD Conference
  on Evolvable Hardware (EH-2005), Washington
  DC, June 29 - July 1, 2005
• Interview at The Scientist Volume 18 Issue
  18 26 Sep. 27, 2004 Alternative Energy
  for Biomotors
• Interview at the http//science.nasa.gov/
• Our research webpage http//www.bionano.neu.ed
  u

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Acknowledgments
NASA Institute of Advanced Concepts (NIAC) Phase
II Grant, September 2004
http//www.niac.usra.edu/             
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Thank You